Hello.
I can confirm, subfolders are not synced, only files within the folder. Neither with the regular … > synchronize nor via the new two way sync ( … > Details > checkbutton synchronize)
And yes IMO this need to be fixed.
Personally I cannot do anything to speed this up.
Best is to leave a 
on the github issue Sync folders + subfolders · Issue #269 · nextcloud/android · GitHub
The devs regularly look at the issues with the most
(Do not comment “+1” or similar in github)
If you have a Nextcloud subscription, open a ticket in portal.nextcloud.com
Or maybe come to the community conference and talk to the Android team Nextcloud Community Conference 2025 - Nextcloud
Also related: Allow 2-way-sync · Issue #19 · nextcloud/android · GitHub
Yours
alexanderdd